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A Manhattan jury has found Pedro Hernandez guilty of murder in the 1979 disappearance of 6-year-old Etan Patz, bringing to an official close a notorious case that transfixed New Yorkers for over three decades.

The verdict on Tuesday came on the ninth day of deliberations after a three-month retrial. The first trial of Hernandez, 54, of Maple Shade, New Jersey, a clerk at a bodega in the SoHo neighborhood where Etan disappeared, ended with a jury deadlocked 11-1 for conviction in 2015.

Hernandez was identified as a suspect by a relative in 2012 and later confessed to police. But his defense said the confession was a fantasy stemming from a mental problem, and argued that the real culprit was a convicted child molester who had a link to Etan’s family.

Etan disappeared on May 25, 1979, while on his way to catch a school bus that stopped outside the corner bodega where Hernandez worked. His mother, Julie Patz, in emotional testimony, said it was his first time walking to the bus stop alone and that he had $1 to buy a treat at the bodega.

He never came home, and an intense police dragnet in the neighborhood never turned up a body, or forensic evidence of a crime, or witnesses who recalled seeing him at the bus stop. The case became a cautionary tale for parents, and Etan’s picture was put on milk cartons as part of a nascent national movement to find missing children.

In the 1980s, attention in the case focused on Jose Ramos, a convicted child molester who is now serving time in Pennsylvania. Ramos had a social relationship with a woman who walked Etan home from school during a bus strike.

Ramos intrigued authorities by telling them that he had an encounter with a boy who could have been Etan on the day he vanished, and also made incriminating remarks to two informants who were placed in jail with him. But he never confessed and was never prosecuted.

Hernandez, according to testimony at trial, made incriminating statements that varied in their details to a prayer group, an ex-wife and a friend. After a lengthy unrecorded interrogation by the NYPD in 2012, he recorded purported confessions for police and prosecutors.

He said that he had lured Etan into the basement of the bodega by offering him a soda, strangled him to death, packed his body into a produce box and lugged it to a dumpster two blocks away. He did not give a motive, saying only that “something took over me,” but prosecutors believe he tried to sexually assault the 6-year-old.

Both trials were hotly contested. Prosecutors portrayed Hernandez as the missing piece in a jigsaw puzzle — a man at the right place at the right time who put the body in a dumpster where it would have been trucked to a landfill before Etan’s parents ever knew he was missing, and who left New York and sought forgiveness at a religious retreat within weeks of the disappearance.

The defense, however, portrayed Ramos as a far more likely suspect — a man with a string of molestation charges unlike Hernandez, a father whose record was clean except for the Patz allegations. A former FBI supervisor who investigated Ramos testified that she believed he was guilty.

The defense called mental health experts — whose conclusions were contested by prosecution experts — to testify that Hernandez had low IQ and suffered from schizotypal personality disorder, a mild form of schizophrenia, that could have produced delusions stemming from his own horrific childhood of abuse.

In a case with no body and no forensic evidence to even prove Etan was killed, the defense also hammered on inconsistencies in Hernandez’s purported confession. He said Etan had no hat, but Etan was wearing a hat when he left home. He said he had thrown a pencil bag Etan was carrying behind a refrigerator, but it was never found in the basement.